## # cytoBands ## track cytoBandIdeo longLabel Chromosome ideogram with cytogenetic bands shortLabel cytoBandIdeo bigDataUrl cytobands/cytoBandIdeo.bigBed type bigBed ## # map ## track gap shortLabel Gap longLabel Gap Locations group map visibility hide type bigBed 3 bigDataUrl gap.bigBed priority 1 track gc5Base shortLabel GC Percent longLabel GC Percent in 5-Base Windows group map visibility hide autoScale Off maxHeightPixels 128:36:16 graphTypeDefault Bar gridDefault OFF windowingFunction Mean color 0,0,0 altColor 128,128,128 viewLimits 30:70 type bigWig 0 100 bigDataUrl gc5Base.bigWig html gc5Base include validation.trackDb.txt trackk mappability shortLabel Mappability longLabel Mappability group map visibility hide type bigWig 0 200 bigDataUrl mappability/mappability_chm13v1_200bp.bw track kmers shortLabel K-MERs longLabel K-MERs superTrack on hide visibility hide group map priority 100 track kmers21bed parent kmers shortLabel Tandem 21-MERs longLabel Tandem 21-MER group map visibility hide type bigBed 4 bigDataUrl kmers/kmers-21-tandem.bigBed priority 1 html kmersTandem.html track kmers21wig parent kmers shortLabel Tandem 21-MER density longLabel Tandem 21-MER density group map visibility hide type bigWig 0 100 bigDataUrl kmers/kmers-21-tandem.bigWig priority 2 html kmersTandem.html track kmers21uniq parent kmers shortLabel Unique 21-MERs longLabel Unique 21-MERs group map visibility hide type bigBed 3 bigDataUrl kmers/kmers-21-uniq.bigBed priority 3 html kmersUniq.html track kmers51uniq parent kmers shortLabel Unique 51-MERs longLabel Unique 51-MERs group map visibility hide type bigBed 3 bigDataUrl kmers/kmers-51-uniq.bigBed priority 4 html kmersUniq.html track illuminaMarkerDeserts shortLabel Marker Deserts longLabel Illumina Marker Deserts group map visibility hide type bigBed 4 bigDataUrl illuminaMarkerDeserts.bigBed ## # varRep ## track rmskV2 shortLabel RepeatMasker V2 longLabel Repeating Elements by RepeatMasker V2 group varRep visibility hide itemRgb on maxItems 1000000 maxWindowToDraw 100000000 type bigBed 9 + bigDataUrl rmskV2/rmskV2.bigBed priority 1 track compositeRepeats shortLabel Composite Repeats longLabel Composite Repeats group varRep visibility hide maxItems 1000000 maxWindowToDraw 100000000 type bigBed 4 bigDataUrl compositeRepeats/compositeRepeats.bigBed priority 1.05 track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility hide type bigBed 4 + bigDataUrl trf/trf.bigBed priority 2 track sedefSegDups compositeTrack off shortLabel SEDEF Segmental Dups longLabel Segmental Duplications priority 10 group varRep type bigBed 9 track sedefSegDupsAll parent sedefSegDups shortLabel SEDEF Segmental Dups longLabel Segmental Duplications group varRep visibility pack itemRgb on maxItems 100000 type bigBed 9 bigDataUrl sedefSegDups/chm13.draft_v1.0_plus38Y.SDs.bed.bb priority 1 html sedefSegDups.html track sedefSegDupsLow parent sedefSegDups shortLabel SEDEF Segmental Dups Low Id longLabel SEDEF Segmental Duplications Low Identity group varRep visibility hide itemRgb on maxItems 100000 type bigBed 2 bigDataUrl sedefSegDups/chm13.draft_v1.0_plus38Y.SDs.lowid.bed.bb html sedefSegDups.html priority 7 html sedefSegDups.html include hg002_hifiasm.trackDb.txt include hg00733_hifiasm.trackDb.txt include wssd.trackDb.txt ## # cenTelo ## track cenRegions shortLabel Centromere Regions longLabel Centromere Regions group cenTelo type bigBed visibility hide color 218,165,32 bigDataUrl cenSatRegions.bigBed priority 1 track cenSatAnnotation shortLabel CenSat Annotation longLabel Centromeric Satellite Annotation group cenTelo visibility hide itemRgb on maxItems 100000 type bigBed 9 + bigDataUrl cenSatAnnotation.bigBed priority 2 track newSatellitesMonomersArrays shortLabel New Satellites longLabel New Satellites Monomers Arrays group cenTelo visibility hide itemRgb on maxItems 100000 type bigBed 4 bigDataUrl newSatellitesMonomersArrays/newSatellitesMonomersArrays.bigBed priority 3 include alphaSatHOR.trackDb.txt # track hors # shortLabel HORs annotation # longLabel Centromere HORs annotation # group cenTelo # visibility hide # itemRgb on # maxItems 100000 # type bigBed 9 # bigDataUrl hors.bigBed # priority 5 # # track superHors # shortLabel Super HORs annotation # longLabel Centromere Super HORs annotation # group cenTelo # visibility hide # itemRgb on # maxItems 100000 # type bigBed 9 # bigDataUrl superHors.bigBed # priority 6 # # track AS_HOR_Annot # shortLabel AS HOR annotation # longLabel Alpha satellite higher-order repeats annotation # group cenTelo # visibility hide # type bigBed 9 # itemRgb on # maxItems 100000 # bigDataUrl as_annotation/AS_HOR_Annot.bigBed # priority 10 # # track AS_SF_Annot # shortLabel AS SF annotation # longLabel Alpha satellite suprachromosomal Families and pericentromeric monomer layers annotation # group cenTelo # visibility hide # type bigBed 9 # itemRgb on # maxItems 100000 # bigDataUrl as_annotation/AS_SF_Annot.bigBed # priority 11 # # track AS_strand # shortLabel AS strand # longLabel alpha satellite higher-order repeats strand orientation # group cenTelo # visibility hide # type bigBed 9 # itemRgb on # maxItems 100000 # bigDataUrl as_annotation/AS_strand.bigBed # priority 12 # ## # genes ## include CAT_V4/trackDb.txt include crispr.trackDb.txt track liftOffV2 bigDataUrl liftOffV2/liftOffV2.bigGenePred shortLabel LiftOff Genes V2 longLabel LiftOff Genes V2 type bigGenePred group genes priority 10 labelFields name, geneName, name2 defaultLabelFields geneName searchIndex name,name2,geneName track liftOffGenes compositeTrack off visibility hide shortLabel LiftOff Genes V1 longLabel LiftOff Genes Annotations V1 based on GENCODE type bigGenePred group genes priority 800 track liftOffGenesAll parent liftOffGenes on bigDataUrl liftOffGenes/chm13.draft_v1.0_plus38Y.all.bb shortLabel LiftOff Genes V1 (All) longLabel LiftOff Genes V1 - all annotations type bigGenePred group genes labelFields name, name2 defaultLabelFields name searchIndex name,name2 track liftOffGenesOrf parent liftOffGenes on bigDataUrl liftOffGenes/chm13.draft_v1.0_plus38Y.orf_only.bb shortLabel LiftOff Genes V1 (ORFs) longLabel LiftOff Genes V1 - annotations with ORFs type bigGenePred group genes labelFields name, name2 defaultLabelFields name searchIndex name,name2 track gencodeBlat shortLabel GENCODE BLAT longLabel BLAT of GENCODE RNAs html gencodeBlat.html group genes type bigPsl priority 15 color 0,0,100 canPack on visibility hide baseColorDefault diffCodons baseColorUseCds given baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 labelFields name,geneSym,geneId,geneType defaultLabelFields geneSym labelSeparator " " bigDataUrl gencodeBlat.bigBlatPsl searchIndex name,geneSym,geneId track refSeqBlat shortLabel RefSeq BLAT longLabel BLAT of RefSeq curated RNAs html refSeqBlat.html group genes type bigPsl priority 16 color 0,0,100 canPack on visibility hide baseColorDefault diffCodons baseColorUseCds given baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 labelFields name,geneSym,geneId,geneType defaultLabelFields geneSym labelSeparator " " bigDataUrl refSeq-curated.bigBlatPsl searchIndex name,geneSym,geneId,geneType ## # comparative genomics ## include cactus.trackDb.txt include grch38Lastz.trackDb.txt track grch38Synteny25kb shortLabel GRCh38 Synteny 25KB longLabel GRCh38 Synteny 25KB resolution type bigPsl color 0,20,180 visibility hide priority 40.1 bigDataUrl synteny/synteny.25kb.bigPsl group compGeno html synteny.html track grch38Synteny1mb shortLabel GRCh38 Synteny 1MB longLabel GRCh38 Synteny 1MB resolution type bigPsl color 0,20,180 visibility hide priority 41.1 bigDataUrl synteny/synteny.1mb.bigPsl group compGeno html synteny.html track chm13_uncovered_byGRCh38 shortLabel GRCH38 non-syntenic longLabel GRCh38 non-syntenic group compGeno visibility hide type bigBed 3 bigDataUrl grch38NonSyntenic/chm13_v1.0_uncoveredByGRCh38WinnowmapAlignments.bigBed priority 50 ## # Expression/transcription/rna ## include proSeq3.trackDb.txt include proSeqDefault.trackDb.txt include rnaSeq3.trackDb.txt include rnaSeqKmerFilt2.trackDb.txt #include cutnrun.trackDb.txt #include cutnrun-losalt.trackDb.txt #include cutnrun-kmer-enrichment.txt track salmonQuantV4 shortLabel Salmon expression longLabel Salmon Transcript-level expression estimates (CAT V4) group rna visibility hide itemRgb on maxItems 100000 type bigBed 12 bigDataUrl CHM13.CATv4.salmonQuant.bb priority 8 ## # regulation ## include methylation.txt include chm13_epigenetics.txt include hg002_epigenetics.txt track jaspar shortLabel JASPAR TFBS longLabel JASPAR TFBS group regulation visibility hide type bigBed 6 bigDataUrl jaspar/jaspar.bigBed priority 4 html jaspar.html track cpgIsland shortLabel CpG Islands longLabel CpG Islands (Islands < 300 Bases are Light Green) group regulation visibility hide color 0,100,0 altColor 128,228,128 type bigBed 4 + priority 5 bigDataUrl t2t-chm13-v1.0.cpgIslandExt.bb include encode_macs2.trackDb.txt